Seeing the spark you've added to the debate, here are more reasons as to why Cortana is clearly 'changed' post-library plunge and now a hitch-hiking convict.

- The much mentioned red eyes and aggressive change in tone towards masterchief after access to the library info.

- The level title 'Two Betrayls': we know one betrayl is 343GS misleading MC with the information he supplies him. The other... well the only other person involved in the exchange is Cortana.

- The level sub-heading 'Breaking Stuff to look Tough': To look tough alone is to imply there is no real substance or meaning to the act. Cortana orders us to destroy those plasma power cells becasue 343GS might still activate Halo without the index. THIS MAKES NO SENSE.
1. His protocols mean he can't activate Halo himself, hence his interest in chief.
2. He obviously DOES requires the index - why lead MC thru the library? Why chase MC around, demand he be killed, why why why if there is a possibility of firing the Halo without it.

If we make the logical assumption (this is indeed an act of destruction with no inherent reason for us the player) this again adds weight to the idea that Cortana is destoying Halo for reasons OTHER than saving humanity.

-Cortana demonsrates some pretty remarkable talents that suggest an evolution far beyond that of her previous 'ship AI' post. Remember, just becuase you read about something doesn't mean you should be a ble to do it. This applies to Cortana in the forerunner database.

1. She makes the index dissapear - a material object. She does not teleport it - there is no characteristic yellow glow and it is clearly impossible for 343GS to go and get it. This is a stupendous, dimension manipulating talent.

2. She shuts down 343GS, a guard AI made by a massively advanced civilisation. This is like a Victorian chamber-maid reading a contemproary book on the internet and then successfuly hacking into FBI servers.

3. She is able to teleport - this is, as far as I know, a skill human civilisation is completely unable to emulate. If not why do we run over to see Keyes in the games opening and not just teleport straight there? I understand that she learns of a telportation network from the library info, but this is a skill she shouldn't be able to physically 'do' - what human created programs could possibly interact with an alien mechanism that manipulates something not even invented yet? The victorian chamber-maid analogy springs to mind.

This is just in-game evidence. The Cortana Poems make it pretty conclusive that there is some identity confusion going on - infact they appear to suggest she has managed to reach a forth stage of rampancy (which is near Godhood is it not?)

As to why and what is going on... well I have a number of ideas in my head having read some william blake and a bit of Genesis.

By sharp and flame,

Cortana

In the bible, when Adam and Eve are kicked out of Eden and no longer its guardians, heavenly creatures and a burning sword are left as protectors. I feel that Cortana is clearly this burning sword - or more precisely she is consumed by this 'burning sword' that lies dormant in the network and claims her identity. In the letter she mentions how this other AI has an unhealthy preocuupation with my mother. If we deduce the other AI is 343 then how can he have a preoccupation with Cortana's mother? Who is the mother?

Well lets bring in William Blake - references to his work are peppered throughout Cortana's writing.

Blake is rather obsessed with worms - and on numerous occasions he states
that the worm is 'His mother and his sister'. I would suggest that the worm (attributed with death, the ability to renew the moisture of the sandy plain, alter the Atmospheres, originate from a 'black shinning sun', and evolve into serpents, as well as being labelled armies of disease) is the flood. We see flood-textured worms in the Silent Cartographer sea and other water sources.

This would make sense - 343 GS is indeed obsessed with the flood - he exists almost exclusively to contain them and would naturally have an unhealthy preoccupation with the flood/worm.

SO Cortana's mother = Blake's worm = flood.

This explains why Cortana would want to destroy Halo - a virtual Jail of the flood and destroyer of its food source.